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The software developer I live with suggested I put in the steps I used that threw up the problem. I did some different things, so:
1) Took existing already made epub anthology, opened it in calibre's editor, tweaked a few tags, refreshed the TOC by using the "T" button (opens up TOC dialogue) deleting existing TOC, clicking "create ToC from all headings" and clicking okay. Then saving the file. I didn't even notice the missing TOC entries until today.
2) Took an unedited epub I made from merging several epubs online where i have never had an issue before. Converted the file through calibre, opened up file in editor. Preexisting ToC (I didn't notice if all files were there). Changed all h1 and h2 tags to h4, hit the ToC button again, deleted existing Toc, hit "create Toc entries from all headings". THEN I noticed the files towards the end of the epub were not showing up in the Toc. If I left them alone, they'd show up, but if I refreshed the ToC even without changing the tags, they'd disappear.
3) Created new, empty epub. Unzipped all the single epubs I had merged into one, importing them into the new "clean" epub, group by group, refreshing the ToC each time. I got to about 100 files before the Toc entries would not show up. Again, it made no difference WHAT h tags they were, if I used the in editor TOC button, the files would not show up.
That original file, from #1, ALL the ToC entries HAD been there before I updated, I checked a previously backed up version from 3 weeks ago and they were there. They only disappeared AFTER I upgraded.
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